Channel alignment and shift correction
======================================

Check fluorescence registration before interpreting profiles or object
positions. BactoScoop exposes several related operations with different effects.

Object alignment
----------------

``batch_detect_objects(..., align=True)`` uses the object detection alignment
path for the requested channel. The five-channel notebook enables this for
the outer-membrane channel C2 and leaves it disabled for C3–C5. This is an
example-specific choice.

Shifted geometry
----------------

``batch_shift_correction`` constructs shifted contours, midlines, and meshes.
``use_shifted_contours=True`` selects stored shifted geometry in feature
calculation. It requires the relevant shifted data to exist; enabling the flag
does not itself perform shift correction.

Signal cropping
---------------

``shift_signal=True`` activates signal handling during supported measurements.
The profiling and membrane implementations use their respective cropping and
optional-shift utilities. The ``objects`` method receives extra positional
arguments through ``*args`` and does not use ``shift_signal`` as a general
object-coordinate transformation.

Inspect these operations separately because a successful field match does
not prove subpixel registration, and changing one flag does not automatically
change every measurement. See the C2 alignment figure in
:doc:`../examples/five-channel` and the exact API signatures in
:doc:`../reference/parameters`.

.. code-block:: python

   import bactoscoop.plot as bplt
   fig = bplt.plot_C2_alignment(
       ic.image_objects[0], cell_id=43, channel="C2",
       channel_label="Outer membrane", show_objects=True,
   )

Choose a cell ID present in your own retained image before calling a cell-level
plot. The number above comes from the supplied five-channel walkthrough.